For general questions or debugging development errors as a result of using DataJoint, a framework for scientific workflow management. For assistance with debugging, please include: Client OS, DataJoint Client (Python|MATLAB|LabBook|Pharus), DataJoint Version, and Database Version (MySQL 5.7|MariaDB 10.5|etc).
Questions tagged [datajoint]
50 questions
3
votes
1 answer
Datajoint LabBook - how to change ports
I am running Datajoint LabBook through the provided docker container (https://datajoint.github.io/datajoint-labbook/user.html#installation) and wondered whether there is a way to move it away from the (default?) port (80?). I am not sure I…
Horst
- 167
- 1
- 6
3
votes
1 answer
What is the correct ORDER BY syntax in DataJoint for Python?
In DataJoint for Python, what is the correct syntax of the ORDER BY argument used in the fetch command?
The current documentation (as of 2018-08-17) only specifies the following syntax for DataJoint in MATLAB:
s = fetch(experiment.Session, '*',…
Vathes
- 61
- 6
2
votes
0 answers
How do I migrate my database schema in a backwards-incompatible way with DataJoint?
I work with a neuroscience lab that uses DataJoint and a shared lab database to manage our data and data pipelines during data preprocessing and analysis. We have tables for different data types, both raw and processed, and as we use new hardware…
Ryan Ly
- 41
- 2
2
votes
0 answers
external storage table already exists error datajoint matlab
Whenever I want to create a table with multiple external storage fields I get the following error:
Table '~external_behavior_time_spatial_blobs' already exists
This is a code snippet of the table I am trying to declare:
%{
-> acquisition.Session
->…
Alvaro Luna
- 21
- 1
2
votes
0 answers
DataJointError: Class ________ is not properly declared (schema decorator not applied?) when trying to diagram
DataJoint version 0.13.4
Python 3.9, running in PyCharm 2022.1.1 Pro Edition
MacOS 12.3.1
I've been working with several of the datajoint-elements packages just trying to get an overall schema created so I can see what new schema's, if any, need to…
Spider Pig 212
- 21
- 3
2
votes
1 answer
Is it possible to implement such that it utilizes instead of ?
Is it possible to implement populate such that it utilizes insert instead of insert1 ?
For large data sets, I am getting a server time out error as using insert1 takes hours to populate a table. Here is what I have for:
def make(self, key):
…
Juux
- 21
- 3
2
votes
2 answers
DataJoint: IntegrityError while dropping table
I am in the process of designing our database and have a table called Session in the common_exp schema with the following definition:
@schema
class Session(dj.Manual):
definition = """ # Information about the session and experimental setup
…
Hendrik Heiser
- 23
- 2
2
votes
1 answer
Dependency from a part table, but not its master table, to an upstream table suddenly fails
I have a table Downstream with a part table DownstreamPart. DownstreamPart, but not Downstream, has a dependency to an upstream table Upstream (the only other additional dependency is to Downstream). This setup has worked so far, correctly…
lara
- 21
- 2
2
votes
1 answer
Use a docker image to build a different docker image using a dockerfile
I am trying to build a docker image of a flask app using a docker file. The flask app uses a docker image of specific sql version datajoint/mysql (using docker-compose). But I get the following error:
/bin/sh: 1: docker: not found
The command…
ishaan arora
- 523
- 8
- 18
1
vote
1 answer
Moving files within a datajoint filestore
We have a file store set up for analysis files, and we've realized that we need to create a subdirectory structure within in. The dj.config settings are below, and the schema definition is
@schema
class AnalysisNwbfile(dj.Manual):
definition =…
Loren Frank
- 43
- 2
1
vote
1 answer
Storing wide-form dataframes in datajoint table
Say I have some analysis that spits out a wide-form pandas dataframe with a multiindex on the index and columns. Depending on the analysis parameters, the number of columns may change. What is the best design pattern to use to store the outputs in a…
zagaroo
- 31
- 4
1
vote
0 answers
What’s the best way to profile python code when using datajoint?
We have tried using line_profiler in juypter but it just tells us that the auto populate function is using all of the cpu time. Is there a simple way for us to get a more detailed profiling report from a .populate() call?
Loren Frank
- 43
- 2
1
vote
1 answer
`delete()` vs. `fetch()` with underspecified relative restrictions
My database has a number of sessions.
@schema
class Session(dj.Manual):
definition = """
-> Subject
session_datetime: datetime
"""
I could fetch or delete them as follows.
total_sessions = session.Session #…
Chris Broz
- 136
- 8
1
vote
1 answer
Does datajoint "join" operator require tables to have the same value at shared secondary attributes?
I am a researcher in Loren Frank's lab at UCSF. When calling populate on a Computed datajoint table that depends on two upstream tables which have entries that have the same value for shared primary attributes but different values for a shared…
jguides
- 27
- 4
1
vote
0 answers
InvalidXMLError: InvalidXMLError: message: "BucketLocationConstraintResult" XML is not parsable
I am setting up a local database for datajoint following instructions here: https://github.com/datajoint/mysql-docker.
The mySQL database works but now I wanted to use MinIO for external storage. I fire up MySQL and MinIO as services using…
user72328
- 11
- 1